AMBER Archive (2006)

Subject: AMBER: Release of RESP ESP charge DDatabase

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Jan 16 2006 - 10:04:47 CST

Dear Amber users,

I am pleased to announce the release of the RESP ESP charge DDataBase (or
R.E.DD.B.) @ http://www.u-picardie.fr/labo/lbpd/REDDB/.

RESP and ESP charges centered on atoms are needed in many molecular mechanics
and docking studies, and used in many force field based simulations. These
atomic charges are recognized as highly efficient to reproduce many molecular
properties. However, no real system allows to rigorously define the charge
derivation conditions, and store, compare and distribute the corresponding
charge values.

The RESP ESP charge DDataBase is a new source of RESP or ESP charge values for
small structures and model systems. Its goals are multiple. R.E.DD.B. allows to
freely store and distribute RESP and ESP charges of high quality and high
reproduciblility in the scientific community. However, R.E.DD.B. can also be
seen as a tool devoted to reproduce, compare, criticize and improve the
different RESP and ESP models. Many different procedures are used to derive
such RESP or ESP charges, and the charge values are affected by many parameters
(QM programs, algorithms, molecular orientation, molecular conformation, human
errors, etc...). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but
also the structures (Cartesian coordinates optimized by QM) and detailed
information about the method used to derive the charges.

Two types of the data or projects can be found in R.E.DD.B.
* WHOLE MOLECULE type projects, "W-$n", which corresponds to an intact
(un-broken) molecule. Examples are small organic or inorganic molecules such as
solvent molecules (Dimethylsulfoxide, Ethanol, Cyclohexane etc...), or ligands
of proteins or nucleic acids.
* MOLECULE FRAGMENT type projects, "F-$n", which corresponds to a part (or
fragment) of an organic or inorganic macro-molecule. Examples are amino-acid
fragments 'NH-CH(R)-CO' (AA) where the atomic charges are generally derived
using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from
the fusion between dimethylphosphate and the corresponding nucleosides, or
monosaccharide fragments. These fragments are generally compatible with
previously existing ones (available in force field topology databases), and
used to construct macro-molecules such as proteins, nucleic acids or
polysaccharides.

DESCRIPTION OF R.E.DD.B.:
- A R.E.DD.B. project code is automatically attributed to each project submitted
in R.E.DD.B. once it has been sucessfully uploaded. This code should to be used
by its author(s) to reference the R.E.DD.B. project in the corresponding
publication. Consequently, the R.E.DD.B. project code provides a rigorous link
between the charge values and the corresponding publication insuring the
definition/reproducibility of the published results.

- A tool has been developped allowing the author(s) of a project (i) to fully
describe the computational conditions she/he used in the charge derivation
procedure and (ii) to upload the files required to characterize this project.

- A second tool has been written to efficiently search projects within R.E.DD.B.
and download the corresponding projects.

- FAQ are available to describe the project submission procedure, the data and
files required for a submission, the ways of searching projects in R.E.DD.B.
and much more.

- A list of references about RESP and ESP charges is also available.

- Each whole molecule and molecule fragment and its corresponding charge values
is visualized within HTML pages using the Jmol program,
http://jmol.sourceforge.net/, and J2SE Runtime Environment,
http://java.sun.com/j2se/1.5.0/download.jsp.

- For each molecule name and project name provided in a project a link to
Wikipedia, the Free Encyclopedia, http://en.wikipedia.org/wiki/Main_Page/ is
generated providing general information.

- The R.E.DD.B.2t ("bis & test") internet site,
http://www.u-picardie.fr/labo/lbpd/REDDB2t/ has been designed to track bugs in
the system. It can also be used by anyboby interested in learning how to submit
projects in the official RESP ESP charge DDatabase. Thus, this "bis & test" web
site is useful for knowing the information required before/for an official
R.E.DD.B. by performing and recording blind tests.

EXAMPLES OF PROJECT AVAILABLE IN R.E.DD.B.:
We have already submitted close to 140 projects involving multi-orientation,
multi-conformation and/or multi-molecule RESP or ESP fit. Below, is a short
listing of some projects available in R.E.DD.B.:

* RESP atomic charges for 10 solvent molecules based on the Connolly surface
algorithm and the HF/6-31G* theory level: Project "W-46",
http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-46/info.html with many links to
Wikipedia: http://en.wikipedia.org/wiki/Organic_solvent,
http://en.wikipedia.org/wiki/Ethanol,
http://en.wikipedia.org/wiki/Dimethylsulfoxide etc...

* RESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and
the HF/6-31G* theory level: Project "W-47".

* ESP atomic charges for 10 solvent molecules based on the Connolly surface
algorithm and the HF/6-31G* theory level: Project "W-48".

* ESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and
the HF/6-31G* theory level: Project "W-49".

* RESP atomic charges for the 4 DNA and RNA nucleosides based on the Connolly
surface algorithm and the HF/6-31G* theory level: Projects "W-69" and "W-74".

* RESP atomic charges for the 4 DNA and RNA nucleosides based on the CHELPG
algorithm and the HF/6-31G* theory level (following a strategy similar to that
applied in the GLYCAM 2004 force field, http://glycam.ccrc.uga.edu/index.jsp):
Projects "W-73" and "W-78".

* RESP atomic charges for the central, (+)NH3-terminal, (-)OOC-terminal,
NH2-terminal and HOOC-terminal fragments of the dimethylalanine amino acid
based on the Connolly surface algorithm and the HF/6-31G* theory level: Project
F-3, http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-3/info.html and Projects
"F-7", "F-11", "F-15" "F-19", respectively.

* Similar data are available for the O-methyl-L-tyrosine amino acid,
http://www.scripps.edu/newsandviews/e_20011029/schultz1.html involving the
Connolly surface and the CHELPG algorythm (RESP and ESP charges): Projects
"F-23" up to "F-44".

* RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G*
theory level for the 16 components of a force field topology database useful
for modeling regular DNA: Project "F-45",
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/info.html with a LEaP script,
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/leaprc-mol2tooff.ff to convert
the library precursors (Tripos format) into OFF files.

* RESP atomic charges based on the CHELG algorithm and the HF/6-31G* theory
level for the 16 components of a force field topology database useful for
modeling regular DNA (following a strategy similar to that applied in the
GLYCAM 2004 force field): Project "F-49".

* Same as project F-45, but the phosphate is located at the O3' position instead
of the O5' one: Project "F-50".

* RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G*
theory level for the 16 components of a force field topology database useful
for modeling regular RNA: Project "F-51" with a LEaP script to convert the
library precursors (Tripos format) into OFF files (up to "F-56" for other RNA
force field topology databases).

* Unusual nucleotide projects: "F-57", "F-58" and "F-59".

More projects are available, see the download section...

These projects have been carried out using the R.E.D. program (version III),
http://www.u-picardie.fr/labo/lbpd/RED/. We hope the community will find
R.E.DD.B. interesting and will participate to its development. We encourage
researchers to submit projects in R.E.DD.B. involving multi-orientations,
multi-conformations and multi-molecules and not only single-orientation,
single-conformation and single molecule projects which are more limited.

This email is available @ http://www.u-picardie.fr/labo/lbpd/REDDB/release.php
with all the links to the R.E.DD.B. projects reported.

Best regards, Francois 

-- 
 * F.-Y. Dupradeau *
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
       ****
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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